Nearest-Neighbor Analysis

Part of the Methods in Molecular Biology™ book series (MIMB, volume 200)


Nearest-neighbor analysis can be used to identify the 3′ nearest neighbors of 5mC residues in DNA (1,2). It can also be used to measure the level of methylation of a specific methylated dinucleotide in DNA. Typically, in the case of mammalian DNA, this means quantifying the degree of methylation at CpG dinucleotides. It has the added advantage of being applicable to small samples of the order of 1 microgram of genomic DNA. The only drawback is that it is a radioactive technique and the appropriate facilities and techniques for handling radioactive substances must be available.


Fume Hood Klenow Fragment Isobutyric Acid Micrococcal Nuclease Geiger Counter 
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    Lyko, F., Ramsahoye, B. H., and Jaenisch, R. (2000) DNA methylation in Drosophila melanogaster. Nature 408, 538–540.PubMedCrossRefGoogle Scholar
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    Ramsahoye, B. H., Biniszkiewicz, D., Lyko, F., Clark, V., Bird, A. P., and Jaenisch, R. (2000) Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc. Natl. Acad. Sci. USA 97, 5237–5242.PubMedCrossRefGoogle Scholar
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    Gruenbaum, Y., Stein, R., Cedar, H., and Razin, A. (1981) Methylation of CpG sequences in eukaryotic DNA. FEBS Lett. 124, 67–71.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc. 2002

Authors and Affiliations

  1. 1.Department of HaematologyWestern General HospitalEdinburghUK

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